Search Results for "sequence scaffold, java" - Page 4

Showing 186 open source projects for "sequence scaffold, java"

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  • 1
    A tool to compare microbial genomes by their sequence fragments. We redistributed the Bioperl package in our software for convenience purpose. The latest Bioperl package can be downloaded from: http://www.bioperl.org. System Requirement: Java Runtime Environment 1.6.0 or above; Perl 5.0 or above If you have any difficulties to run this tool, just let me know by chenh12@nyumc.org.
    Downloads: 0 This Week
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  • 2

    Genome Microsatellite Analyzing Tool

    GMATO : Microsatellite Analyzing Tool for Huge Genome at any size

    The increasing sequence availability of more and more huge whole genomes (>1G) defeated currently existing SSR analyzing tools. Genome-wide Microsatellite Analyzing Tool (GMATo) is a novel powerful program for faster SSR mining at any length, any size,and comprehensive statistical analysis at genome aspect, especially designed for huge genome based on Perl scripts. Only one input file is required which contains DNA sequences in raw fasta format and output files in tabular format list all SSR...
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  • 3
    NSIT

    NSIT

    Novel Sequence Identification Tool

    NSIT (Novel Sequence Identification Tool) is an efficient software for identifying novel sequences in a de novo human genome assembly. Novel sequences are defined as DNA sequences in the de novo assembly that are longer than 100 bp, not known-repeats, and not present in the reference assembly. NSIT was written in C++ and runs on both 32-bit and 64-bit Linux machines. It requires about 2 GB of RAM. NSIT comes with a JAVA graphical viewer which can be used to view how the identified novel...
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  • 4

    DimerRemover

    Remove adapter dimers from NGS data

    This program can be used to count or remove adapter dimers in fastq files. Using a provided adapter sequence, it generates variations of this sequence and stores them in a hash table. The reads can then be directly matched against the hash. It is far more time efficient than doing alignment.
    Downloads: 0 This Week
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  • 5
    ProbeMaker is a framework for design of sets of oligonucleotide probes. It allows the design of different types of probes made up of separate sequence elements. A Plug-in mechanism allows extension of the framework with new functionalities.
    Downloads: 5 This Week
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  • 6
    SecStAnT

    SecStAnT

    Secondary Structure Analysis Tool for data selection and statistics

    SecStAnT is a tool for the automatic creation of data-sets of structures from Protein Data Bank (PDB) with user-defined structural composition, and for the calculation of their internal variables distributions. SecStAnT is able to 1. Select from PDB data sets of structures based on user specified secondary structures (defined based on internal PDB classification or on DSSP) and/or sequence motives. 2. Build Data-sets at different levels of resolution (all atoms, only backbone, only Cα...
    Downloads: 0 This Week
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  • 7
    The MolTools Java library provides tools for building applications that handle nucleotide sequence data. Features include sequence I/O, handling of lists/databases of sequences, calculation of Tm, and other utilities for sequence design.
    Downloads: 0 This Week
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  • 8
    ADOPS

    ADOPS

    Automatic Detection Of Positively Selected Sites

    ADOPS is a bioinformatics tool that automatizes the detection of positively selected sites given a set of unaligned nucleotide sequence data. ADOPS implements a complete workflow that integrates three well-known bioinformatic tools: T-Coffee, MrBayes and Codeml (PAML).
    Downloads: 0 This Week
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  • 9
    KTNotes

    KTNotes

    Speedy formatted advanced note-taking with the Kindle Touch.

    ... installation sequence.
    Downloads: 0 This Week
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  • 10

    SlalomGenerator

    Generator of coherent slalom sequence

    Slalom Generator is small java tools (cross platform) to generate sequence. Indicate figures you know, number of plot, and expected number of figures in sequence and generate !
    Downloads: 0 This Week
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  • 11
    JAVA Program to Sequence Diagram Generator. This tool tries to help on analysing and understanding the behavior of the code when developping JAVA applications by generating the respective Sequence Diagram automatically at program execution.
    Downloads: 0 This Week
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  • 12

    Bowling Score

    Simple Java project to compute the bowling score

    A simple Java project meant to compute the score of a bowling game. Currently implemented: - src/ao.bowling: architecture for the bowling game (a Game can be played by multiple Players, each Player has 10 Frames in which to knock down the pins within 1-3 Throws) - test/ao.bowling: JUnit test cases for a few typical scenarios TODO: - parse&sanitize user input (sequence of numbers representing number of pins knocked down at each throw) - simple swing interface where user inserts data...
    Downloads: 0 This Week
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  • 13
    An assessmemt tool of sequence repeats for short read sequencing.
    Downloads: 0 This Week
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  • 14
    Ferox

    Ferox

    Ferox - Sequence Alignment with Fuzzy K-mers

    Ferox is a DNA sequence alignment application that uses fuzzy k-mers to quickly and accurately align sets of sequence reads against a reference genome. Ferox can also be used to align whole genomes. The seeding mechanism used by Ferox is highly configurable, allowing custom fuzzy seeds to be created declaratively in an XML configuration file.
    Downloads: 0 This Week
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  • 15

    Seurat

    A sequence analysis tool for normal/tumor DNA and RNA data.

    THIS IS NO LONGER THE HOME FOR SEURAT. PLEASE GO TO https://sites.google.com/site/seuratsomatic/ --- Seurat is an sequence analysis program for somatic mutation and allelic imbalance discovery in paired tumor and normal genome and transcriptome data.
    Downloads: 0 This Week
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  • 16

    Jnomics

    Jnomics is a collection of cloud-scale DNA sequence analysis tools

    Jnomics is a collection of cloud-scale DNA sequence analysis tools
    Downloads: 0 This Week
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  • 17
    BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. Please cite the BRIG paper if BRIG is used to generate figures for publications: NF Alikhan, NK Petty, NL Ben Zakour, SA Beatson (2011) BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons, BMC Genomics, 12:402. PMID: 21824423
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    Downloads: 128 This Week
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  • 18
    Firefly UML

    Firefly UML

    A free, easy-to-use and user-friendly Java-based UML editor.

    Firefly UML is a 100% pure Java application designed to create and edit UML conform diagrams. With class diagrams, sequence and instance diagrams, Firefly UML provides a solid selection from the vast range of existing UML diagram types. Firefly UML is really easy to learn as it provides you multiple ways of access to the same function - be it mouse action, hotkey, context menu or toolbar icon. And the best thing is: once you have learned how to handle one type of diagram, you also have learned...
    Downloads: 0 This Week
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  • 19

    video highlighter

    A Java Programme to Grab the Highlights from your Video

    This programme hunts through a long video for Highlights represented by a short black sequence in the clip. This can be created by putting your hand over the lens for a couple of seconds after something good has happened.
    Downloads: 0 This Week
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  • 20
    Pontos

    Pontos

    Pontos calculates distance matrices from DNA sequence alignments.

    Pontos is an easy-to-use, graphical Java program for the calculation of uncorrected distance (or similarity) matrices from DNA sequence alignments in PHYLIP format. It also creates "difference" alignments from regular ones (and vice-versa). It can handle gaps and ambiguities in different ways. Gaps can be: - all used; - all ignored; - ignored only at the ends of the sequences, in a pairwise manner; - ignored only at the ends, but now globally (in effect trimming the whole alignment...
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  • 21
    GenLab abbreviation of Genetics Laboratory .It is a user-friendly bioinformatics tool to support your bioinformatics lab work. GenLab creates a software user-friendly environment, which makes users to make a large number of protein, DNA, and RNA sequence analysis and excellent graphical viewing. It also provides powerful environment for simulations of Protein 3D molecular models. GenLab typically provides: •User-friendly graphical tools used for finding and working with relevant regions...
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  • 22
    Index biological data (genbank sheets, Uniprot...) in a Solr indexer, with index shard support and provides a query interface. Project goal is to create a virtual image with indexer and web interface to query and visualize biological data.
    Downloads: 0 This Week
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  • 23
    JFinisher

    JFinisher

    JFinisher is software for alignment, editing and manipulation DNA seqs

    JFinisher is software for alignment, editing and manipulation of biological sequences. It aims to assist in the finishing of genome assembly. Starting from a reference sequence, the program align contigs using Smith-Waterman local alignment algoritm with auxiliary methods, allowing management of the alignments generated. It has graphical interface for manipulation and visualization of the actions, uniting features that help in editing the sequences. It has internal projects manageable...
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  • 24
    The X Project

    The X Project

    You will canalize the project and determine what will it become.

    Do you know story completion game? Everybody writes a sentence in sequence and nobody knows what will the story be in the end. Would you like to play a code completion game? Write a line of code (or as much as you like) and invite some friends of you to join our game. I started the project with a simple java application produced in Netbeans which does nothing absolutely. I want to learn how much strong the open source comunity is. Let the game begin!
    Downloads: 0 This Week
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  • 25

    Randomizer

    Random sequence generators for Java objects

    Random sequence generators for Java objects, which currently provide you with 3 specialized generators. The simplest of them - Randomizer - gives every Object an equal chance to be selected from the group. The useful RandomizerSet - shuffles the provided Objects and returns the next object in queue once needed. The complex RandomizerMap - Writing a MMORPG? The rarest drop, the better! This beauty is for you. None of them fits your needs? No problem, the parent type RandomSelector...
    Downloads: 0 This Week
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